c pasteurianum  (ATCC)


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    Name:
    Hs 60 Fs
    Description:

    Catalog Number:
    crl-7040
    Price:
    None
    Applications:
    This cell line is neither produced nor fully characterized by ATCC. We do not guarantee that it will maintain a specific morphology, purity, or any other property upon passage.
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    Structured Review

    ATCC c pasteurianum
    Growth, total gas production, hydrogen production, and pH change in Clostridia . Note that all four strains including Clostridium sp., C. acetobutylicum , C. <t>pasteurianum,</t> and C. sphenoides were grown in MSM medium, while C. sphenoides was also in SCM medium (marked with dashed line).

    https://www.bioz.com/result/c pasteurianum/product/ATCC
    Average 93 stars, based on 11 article reviews
    Price from $9.99 to $1999.99
    c pasteurianum - by Bioz Stars, 2020-08
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    Images

    1) Product Images from "Fermentation and Hydrogen Metabolism Affect Uranium Reduction by Clostridia"

    Article Title: Fermentation and Hydrogen Metabolism Affect Uranium Reduction by Clostridia

    Journal: ISRN biotechnology

    doi: 10.5402/2013/657160

    Growth, total gas production, hydrogen production, and pH change in Clostridia . Note that all four strains including Clostridium sp., C. acetobutylicum , C. pasteurianum, and C. sphenoides were grown in MSM medium, while C. sphenoides was also in SCM medium (marked with dashed line).
    Figure Legend Snippet: Growth, total gas production, hydrogen production, and pH change in Clostridia . Note that all four strains including Clostridium sp., C. acetobutylicum , C. pasteurianum, and C. sphenoides were grown in MSM medium, while C. sphenoides was also in SCM medium (marked with dashed line).

    Techniques Used:

    2) Product Images from "Genome-directed analysis of prophage excision, host defence systems, and central fermentative metabolism in Clostridium pasteurianum"

    Article Title: Genome-directed analysis of prophage excision, host defence systems, and central fermentative metabolism in Clostridium pasteurianum

    Journal: Scientific Reports

    doi: 10.1038/srep26228

    Genomic analysis of the central Type I-B CRISPR system of C. pasteurianum . Structure and orientation of CRISPR arrays and cas genes within the genome of C. pasteurianum are shown. Numbers below genes specify locus tags (CP6013 prefix is omitted). Three genes, encoding a putative histidine kinase (CP6013_0531), transposase (CP6013_0532), and a hypothetical protein (CP6013_0533), are located between the 37-spacer CRISPR array and cas genes. Genes encoding the Type I-B Cas proteins are located adjacent to a 37-spacer CRISPR array (spacers are depicted as dark gray boxes). A second 8-spacer CRISPR array (spacers are depicted as light gray boxes) possessing the same 30 nt direct repeat sequence (diamonds) was found elsewhere in the C. pasteurianum chromosome, separated from the cas genes by approximately 2.1 Mbp. The sequence of the common 30 nt direct repeat sequence is shown corresponding to the direction of transcription, which is in opposite directions. A predicted RNA folded structure of the 30 nt direct repeat is shown and compared to the 8 nt 5′ tag of mature crRNA from the C. thermocellum Type I-B system. A putative leader sequence is depicted upstream of the 37-spacer array, while the presence of a similar element within the 8-spacer array is not clear.
    Figure Legend Snippet: Genomic analysis of the central Type I-B CRISPR system of C. pasteurianum . Structure and orientation of CRISPR arrays and cas genes within the genome of C. pasteurianum are shown. Numbers below genes specify locus tags (CP6013 prefix is omitted). Three genes, encoding a putative histidine kinase (CP6013_0531), transposase (CP6013_0532), and a hypothetical protein (CP6013_0533), are located between the 37-spacer CRISPR array and cas genes. Genes encoding the Type I-B Cas proteins are located adjacent to a 37-spacer CRISPR array (spacers are depicted as dark gray boxes). A second 8-spacer CRISPR array (spacers are depicted as light gray boxes) possessing the same 30 nt direct repeat sequence (diamonds) was found elsewhere in the C. pasteurianum chromosome, separated from the cas genes by approximately 2.1 Mbp. The sequence of the common 30 nt direct repeat sequence is shown corresponding to the direction of transcription, which is in opposite directions. A predicted RNA folded structure of the 30 nt direct repeat is shown and compared to the 8 nt 5′ tag of mature crRNA from the C. thermocellum Type I-B system. A putative leader sequence is depicted upstream of the 37-spacer array, while the presence of a similar element within the 8-spacer array is not clear.

    Techniques Used: CRISPR, Sequencing

    The chromosome of C. pasteurianum ATCC 6013. Contig 1 (4,373,654 bp) is depicted as a circular chromosome and shows the approximate location of key genomic features discussed in this study. The two outermost circles indicate locations of gene coding regions (blue) in plus (circle one) and minus (circle two) strands. Genes encoding tRNAs and rRNAs are shown in fuchsia and lavender, respectively. Circle three shows G + C content (deviation from average) and circle four depicts G + C skew in plus (green) and minus (purple) strands. Genome scale is indicated in Mbp on the innermost circle. The CGView Server 120 was used to construct the genome map.
    Figure Legend Snippet: The chromosome of C. pasteurianum ATCC 6013. Contig 1 (4,373,654 bp) is depicted as a circular chromosome and shows the approximate location of key genomic features discussed in this study. The two outermost circles indicate locations of gene coding regions (blue) in plus (circle one) and minus (circle two) strands. Genes encoding tRNAs and rRNAs are shown in fuchsia and lavender, respectively. Circle three shows G + C content (deviation from average) and circle four depicts G + C skew in plus (green) and minus (purple) strands. Genome scale is indicated in Mbp on the innermost circle. The CGView Server 120 was used to construct the genome map.

    Techniques Used: Construct

    Genomic arrangement of key genes and operons involved in the central fermentative metabolism of C. pasteurianum . C. pasteurianum genes and operons (left) are compared with corresponding regulons from related species or key bacteria possessing similar metabolic pathways (right). Select additional copies of C. pasteurianum genes and operons are also depicted (bottom). Locus tags are provided for C. pasteurianum genes (CP6013 prefix is omitted). Metabolic functions of gene products are discussed in detail in the main text. Genes in black and grey depict different directions of transcription. All genes and intergenic regions are depicted to scale.
    Figure Legend Snippet: Genomic arrangement of key genes and operons involved in the central fermentative metabolism of C. pasteurianum . C. pasteurianum genes and operons (left) are compared with corresponding regulons from related species or key bacteria possessing similar metabolic pathways (right). Select additional copies of C. pasteurianum genes and operons are also depicted (bottom). Locus tags are provided for C. pasteurianum genes (CP6013 prefix is omitted). Metabolic functions of gene products are discussed in detail in the main text. Genes in black and grey depict different directions of transcription. All genes and intergenic regions are depicted to scale.

    Techniques Used:

    Overview of the central metabolic pathways of C. pasteurianum based on genomic analysis. Prevalent metabolic pathways leading to production of acids (green), alcohols (blue), and gases (red) are shown derived from commonly employed growth substrates. Many arrows represent multiple enzymatic conversions. The acetone formation pathway is depicted using dashed lines since acetone is not a common product of C. pasteurianum fermentations. The incomplete citrate cycle and other intermediary metabolic pathways are not depicted. Electron bifurcation by the Bcd-EtfAB enzyme complex is shown using 2NADH as reductant. Electron transfer via the EtfAB complex is not shown. Refer to main text for further discussion on central metabolic pathway enzymes and reactions. Abbreviations: EMPP, Embden-Meyerhof-Parnas pathway; N-O PPP, non-oxidative pentose phosphate pathway; MEDP, modified Entner-Doudoroff pathway; CFP, central fermentative pathways; PTS, phosphotransferase system; PMF, proton motive force; GFPC, glycerol facilitator protein channel; Glc, glucose; Suc, sucrose; Fru, fructose; DHA, dihydroxyacetone; 3-HPA, 3-hydroxypropionaldehyde; 1,3-PDO, 1,3-propanediol; GA, glyceraldehyde; FD OX , oxidized ferredoxin; FD RED , reduced ferredoxin.
    Figure Legend Snippet: Overview of the central metabolic pathways of C. pasteurianum based on genomic analysis. Prevalent metabolic pathways leading to production of acids (green), alcohols (blue), and gases (red) are shown derived from commonly employed growth substrates. Many arrows represent multiple enzymatic conversions. The acetone formation pathway is depicted using dashed lines since acetone is not a common product of C. pasteurianum fermentations. The incomplete citrate cycle and other intermediary metabolic pathways are not depicted. Electron bifurcation by the Bcd-EtfAB enzyme complex is shown using 2NADH as reductant. Electron transfer via the EtfAB complex is not shown. Refer to main text for further discussion on central metabolic pathway enzymes and reactions. Abbreviations: EMPP, Embden-Meyerhof-Parnas pathway; N-O PPP, non-oxidative pentose phosphate pathway; MEDP, modified Entner-Doudoroff pathway; CFP, central fermentative pathways; PTS, phosphotransferase system; PMF, proton motive force; GFPC, glycerol facilitator protein channel; Glc, glucose; Suc, sucrose; Fru, fructose; DHA, dihydroxyacetone; 3-HPA, 3-hydroxypropionaldehyde; 1,3-PDO, 1,3-propanediol; GA, glyceraldehyde; FD OX , oxidized ferredoxin; FD RED , reduced ferredoxin.

    Techniques Used: Derivative Assay, Modification, Peptide Mass Fingerprinting, Gas Chromatography

    Effect of substrate degree of reductance on the fermentation product profile of C. pasteurianum . Active metabolic pathways employed by the cell are shown during growth on a range of substrates possessing varied degrees of reductance. General catabolic equations are provided and show the number of moles of reducing equivalents generated (in bold) per two moles of pyruvate formed. Substrates and pathway intermediates are depicted as black and blue diamonds, respectively, while acid and alcohol products are shown as blue circles and squares, respectively. Trace products (
    Figure Legend Snippet: Effect of substrate degree of reductance on the fermentation product profile of C. pasteurianum . Active metabolic pathways employed by the cell are shown during growth on a range of substrates possessing varied degrees of reductance. General catabolic equations are provided and show the number of moles of reducing equivalents generated (in bold) per two moles of pyruvate formed. Substrates and pathway intermediates are depicted as black and blue diamonds, respectively, while acid and alcohol products are shown as blue circles and squares, respectively. Trace products (

    Techniques Used: Generated

    Identification and excision of phage φ6013 from the genome of C. pasteurianum . ( a ) Predicted excision mechanism of phage φ6013 from the genome of C. pasteurianum . Phage excision was induced by exposing exponential phase cultures of C. pasteurianum to 5 μg ml −1 mitomycin C, leading to recombination between attL and attR sites. Sequences corresponding to the core attL and attR φ6013 recombination sites are shown in uppercase. The resulting attP sequence of phage φ6013 is compared to the similar 12 nt core attP site of phage φ3626 from C. perfringens . Prophage excision leads to a circular 42,250 bp phage genome and a single attB scar site within the genome of C. pasteurianum . PCR primers for screening attL , attR , attP , and attB recombination sites are shown, as well as screening primers for long range PCR of the circular excised φ6013 genome. Genomes, genomic regions, and PCR primers are not depicted to scale. ( b ) PCR verification of phage φ6013 excision from the C. pasteurianum chromosome. Orientation and arrangement of PCR primers are depicted in Fig. 1a. Lane 1: marker; lane 2: 904 bp attL product (attLB.S + attL.AS); lane 3: 872 bp attR product (attRP.S + attRB.AS); lane 4: 3,154 bp attP product (attRP.S + attP.AS); lane 5: 1,076 bp attB product (attLB.S + attRB.AS); lane 6: long range PCR marker; lane 7: 22,756 bp 5′ φ6013 product (φ6013.S + attP.AS); lane 8: 22,678 bp 3′ φ6013 product (attRP.S + φ6013.AS). ( c ) Transmission electron microscopy image of phage φ6013 visualized at 245,000× magnification. ( d ) Genomic arrangement of phage φ6013 (42,250 bp). All 52 predicted genes, including some functional assignments, are depicted and are numbered consecutively. Genes in black and grey depict different directions of transcription. The predicted phage attachment site ( attP ) described in the main text is shown. All genes and intergenic regions are depicted to scale.
    Figure Legend Snippet: Identification and excision of phage φ6013 from the genome of C. pasteurianum . ( a ) Predicted excision mechanism of phage φ6013 from the genome of C. pasteurianum . Phage excision was induced by exposing exponential phase cultures of C. pasteurianum to 5 μg ml −1 mitomycin C, leading to recombination between attL and attR sites. Sequences corresponding to the core attL and attR φ6013 recombination sites are shown in uppercase. The resulting attP sequence of phage φ6013 is compared to the similar 12 nt core attP site of phage φ3626 from C. perfringens . Prophage excision leads to a circular 42,250 bp phage genome and a single attB scar site within the genome of C. pasteurianum . PCR primers for screening attL , attR , attP , and attB recombination sites are shown, as well as screening primers for long range PCR of the circular excised φ6013 genome. Genomes, genomic regions, and PCR primers are not depicted to scale. ( b ) PCR verification of phage φ6013 excision from the C. pasteurianum chromosome. Orientation and arrangement of PCR primers are depicted in Fig. 1a. Lane 1: marker; lane 2: 904 bp attL product (attLB.S + attL.AS); lane 3: 872 bp attR product (attRP.S + attRB.AS); lane 4: 3,154 bp attP product (attRP.S + attP.AS); lane 5: 1,076 bp attB product (attLB.S + attRB.AS); lane 6: long range PCR marker; lane 7: 22,756 bp 5′ φ6013 product (φ6013.S + attP.AS); lane 8: 22,678 bp 3′ φ6013 product (attRP.S + φ6013.AS). ( c ) Transmission electron microscopy image of phage φ6013 visualized at 245,000× magnification. ( d ) Genomic arrangement of phage φ6013 (42,250 bp). All 52 predicted genes, including some functional assignments, are depicted and are numbered consecutively. Genes in black and grey depict different directions of transcription. The predicted phage attachment site ( attP ) described in the main text is shown. All genes and intergenic regions are depicted to scale.

    Techniques Used: Sequencing, Polymerase Chain Reaction, Marker, Transmission Assay, Electron Microscopy, Functional Assay

    Related Articles

    other:

    Article Title: Fermentation and Hydrogen Metabolism Affect Uranium Reduction by Clostridia
    Article Snippet: We purchased C. sphenoides (ATCC 19403), C. acetobutylicum (ATCC 824), and C. pasteurianum (ATCC 7040) from the American Type Culture Center (ATCC).

    Article Title: Tequila vinasses acidogenesis in a UASB reactor with Clostridium predominance
    Article Snippet: This strain was also found to be a rapid and efficient glucose fermenter compared to other clostridia strains, such as Clostridium acetobutylicum (ATCC 19403), Clostridium sphenoides (ATCC 19403), and C. pasteurianum (ATCC 7040) (Francis et al. ; Gao and Francis ).

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    ATCC c pasteurianum atcc 6013
    The chromosome of C. <t>pasteurianum</t> ATCC 6013. Contig 1 (4,373,654 bp) is depicted as a circular chromosome and shows the approximate location of key genomic features discussed in this study. The two outermost circles indicate locations of gene coding regions (blue) in plus (circle one) and minus (circle two) strands. Genes encoding tRNAs and rRNAs are shown in fuchsia and lavender, respectively. Circle three shows G + C content (deviation from average) and circle four depicts G + C skew in plus (green) and minus (purple) strands. Genome scale is indicated in Mbp on the innermost circle. The CGView Server 120 was used to construct the genome map.
    C Pasteurianum Atcc 6013, supplied by ATCC, used in various techniques. Bioz Stars score: 93/100, based on 10 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/c pasteurianum atcc 6013/product/ATCC
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    90
    ATCC c pasteurianum
    Genomic analysis of the central Type I-B CRISPR system of C. <t>pasteurianum</t> . Structure and orientation of CRISPR arrays and cas genes within the genome of C. pasteurianum are shown. Numbers below genes specify locus tags (CP6013 prefix is omitted). Three genes, encoding a putative histidine kinase (CP6013_0531), transposase (CP6013_0532), and a hypothetical protein (CP6013_0533), are located between the 37-spacer CRISPR array and cas genes. Genes encoding the Type I-B Cas proteins are located adjacent to a 37-spacer CRISPR array (spacers are depicted as dark gray boxes). A second 8-spacer CRISPR array (spacers are depicted as light gray boxes) possessing the same 30 nt direct repeat sequence (diamonds) was found elsewhere in the C. pasteurianum chromosome, separated from the cas genes by approximately 2.1 Mbp. The sequence of the common 30 nt direct repeat sequence is shown corresponding to the direction of transcription, which is in opposite directions. A predicted RNA folded structure of the 30 nt direct repeat is shown and compared to the 8 nt 5′ tag of mature crRNA from the C. thermocellum Type I-B system. A putative leader sequence is depicted upstream of the 37-spacer array, while the presence of a similar element within the 8-spacer array is not clear.
    C Pasteurianum, supplied by ATCC, used in various techniques. Bioz Stars score: 90/100, based on 11 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 90 stars, based on 11 article reviews
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    85
    ATCC c pasteurianum hyda
    Amino acid sequence alignment of C. <t>pasteurianum</t> <t>HydA</t> (CpA) and C. acetobutylicum HydA (CaA) and HydB (CaB). The ClustalW algorithm was used to generate the alignment, and shading identifies identical (black) and similar (gray) residues. The N-terminal
    C Pasteurianum Hyda, supplied by ATCC, used in various techniques. Bioz Stars score: 85/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    The chromosome of C. pasteurianum ATCC 6013. Contig 1 (4,373,654 bp) is depicted as a circular chromosome and shows the approximate location of key genomic features discussed in this study. The two outermost circles indicate locations of gene coding regions (blue) in plus (circle one) and minus (circle two) strands. Genes encoding tRNAs and rRNAs are shown in fuchsia and lavender, respectively. Circle three shows G + C content (deviation from average) and circle four depicts G + C skew in plus (green) and minus (purple) strands. Genome scale is indicated in Mbp on the innermost circle. The CGView Server 120 was used to construct the genome map.

    Journal: Scientific Reports

    Article Title: Genome-directed analysis of prophage excision, host defence systems, and central fermentative metabolism in Clostridium pasteurianum

    doi: 10.1038/srep26228

    Figure Lengend Snippet: The chromosome of C. pasteurianum ATCC 6013. Contig 1 (4,373,654 bp) is depicted as a circular chromosome and shows the approximate location of key genomic features discussed in this study. The two outermost circles indicate locations of gene coding regions (blue) in plus (circle one) and minus (circle two) strands. Genes encoding tRNAs and rRNAs are shown in fuchsia and lavender, respectively. Circle three shows G + C content (deviation from average) and circle four depicts G + C skew in plus (green) and minus (purple) strands. Genome scale is indicated in Mbp on the innermost circle. The CGView Server 120 was used to construct the genome map.

    Article Snippet: DNA isolation, sequencing, and analysis Total DNA was isolated from C. pasteurianum ATCC 6013 according to a previous method using a Qiagen (Valencia, CA) DNeasy Blood and Tissue Kit.

    Techniques: Construct

    Genomic analysis of the central Type I-B CRISPR system of C. pasteurianum . Structure and orientation of CRISPR arrays and cas genes within the genome of C. pasteurianum are shown. Numbers below genes specify locus tags (CP6013 prefix is omitted). Three genes, encoding a putative histidine kinase (CP6013_0531), transposase (CP6013_0532), and a hypothetical protein (CP6013_0533), are located between the 37-spacer CRISPR array and cas genes. Genes encoding the Type I-B Cas proteins are located adjacent to a 37-spacer CRISPR array (spacers are depicted as dark gray boxes). A second 8-spacer CRISPR array (spacers are depicted as light gray boxes) possessing the same 30 nt direct repeat sequence (diamonds) was found elsewhere in the C. pasteurianum chromosome, separated from the cas genes by approximately 2.1 Mbp. The sequence of the common 30 nt direct repeat sequence is shown corresponding to the direction of transcription, which is in opposite directions. A predicted RNA folded structure of the 30 nt direct repeat is shown and compared to the 8 nt 5′ tag of mature crRNA from the C. thermocellum Type I-B system. A putative leader sequence is depicted upstream of the 37-spacer array, while the presence of a similar element within the 8-spacer array is not clear.

    Journal: Scientific Reports

    Article Title: Genome-directed analysis of prophage excision, host defence systems, and central fermentative metabolism in Clostridium pasteurianum

    doi: 10.1038/srep26228

    Figure Lengend Snippet: Genomic analysis of the central Type I-B CRISPR system of C. pasteurianum . Structure and orientation of CRISPR arrays and cas genes within the genome of C. pasteurianum are shown. Numbers below genes specify locus tags (CP6013 prefix is omitted). Three genes, encoding a putative histidine kinase (CP6013_0531), transposase (CP6013_0532), and a hypothetical protein (CP6013_0533), are located between the 37-spacer CRISPR array and cas genes. Genes encoding the Type I-B Cas proteins are located adjacent to a 37-spacer CRISPR array (spacers are depicted as dark gray boxes). A second 8-spacer CRISPR array (spacers are depicted as light gray boxes) possessing the same 30 nt direct repeat sequence (diamonds) was found elsewhere in the C. pasteurianum chromosome, separated from the cas genes by approximately 2.1 Mbp. The sequence of the common 30 nt direct repeat sequence is shown corresponding to the direction of transcription, which is in opposite directions. A predicted RNA folded structure of the 30 nt direct repeat is shown and compared to the 8 nt 5′ tag of mature crRNA from the C. thermocellum Type I-B system. A putative leader sequence is depicted upstream of the 37-spacer array, while the presence of a similar element within the 8-spacer array is not clear.

    Article Snippet: Spore titers have been reported to differ between seemingly identical strains of C. pasteurianum obtained from different culture collections (ATCC and DSM) , which could reflect variation in levels of excision of φ6013.

    Techniques: CRISPR, Sequencing

    The chromosome of C. pasteurianum ATCC 6013. Contig 1 (4,373,654 bp) is depicted as a circular chromosome and shows the approximate location of key genomic features discussed in this study. The two outermost circles indicate locations of gene coding regions (blue) in plus (circle one) and minus (circle two) strands. Genes encoding tRNAs and rRNAs are shown in fuchsia and lavender, respectively. Circle three shows G + C content (deviation from average) and circle four depicts G + C skew in plus (green) and minus (purple) strands. Genome scale is indicated in Mbp on the innermost circle. The CGView Server 120 was used to construct the genome map.

    Journal: Scientific Reports

    Article Title: Genome-directed analysis of prophage excision, host defence systems, and central fermentative metabolism in Clostridium pasteurianum

    doi: 10.1038/srep26228

    Figure Lengend Snippet: The chromosome of C. pasteurianum ATCC 6013. Contig 1 (4,373,654 bp) is depicted as a circular chromosome and shows the approximate location of key genomic features discussed in this study. The two outermost circles indicate locations of gene coding regions (blue) in plus (circle one) and minus (circle two) strands. Genes encoding tRNAs and rRNAs are shown in fuchsia and lavender, respectively. Circle three shows G + C content (deviation from average) and circle four depicts G + C skew in plus (green) and minus (purple) strands. Genome scale is indicated in Mbp on the innermost circle. The CGView Server 120 was used to construct the genome map.

    Article Snippet: Spore titers have been reported to differ between seemingly identical strains of C. pasteurianum obtained from different culture collections (ATCC and DSM) , which could reflect variation in levels of excision of φ6013.

    Techniques: Construct

    Genomic arrangement of key genes and operons involved in the central fermentative metabolism of C. pasteurianum . C. pasteurianum genes and operons (left) are compared with corresponding regulons from related species or key bacteria possessing similar metabolic pathways (right). Select additional copies of C. pasteurianum genes and operons are also depicted (bottom). Locus tags are provided for C. pasteurianum genes (CP6013 prefix is omitted). Metabolic functions of gene products are discussed in detail in the main text. Genes in black and grey depict different directions of transcription. All genes and intergenic regions are depicted to scale.

    Journal: Scientific Reports

    Article Title: Genome-directed analysis of prophage excision, host defence systems, and central fermentative metabolism in Clostridium pasteurianum

    doi: 10.1038/srep26228

    Figure Lengend Snippet: Genomic arrangement of key genes and operons involved in the central fermentative metabolism of C. pasteurianum . C. pasteurianum genes and operons (left) are compared with corresponding regulons from related species or key bacteria possessing similar metabolic pathways (right). Select additional copies of C. pasteurianum genes and operons are also depicted (bottom). Locus tags are provided for C. pasteurianum genes (CP6013 prefix is omitted). Metabolic functions of gene products are discussed in detail in the main text. Genes in black and grey depict different directions of transcription. All genes and intergenic regions are depicted to scale.

    Article Snippet: Spore titers have been reported to differ between seemingly identical strains of C. pasteurianum obtained from different culture collections (ATCC and DSM) , which could reflect variation in levels of excision of φ6013.

    Techniques:

    Overview of the central metabolic pathways of C. pasteurianum based on genomic analysis. Prevalent metabolic pathways leading to production of acids (green), alcohols (blue), and gases (red) are shown derived from commonly employed growth substrates. Many arrows represent multiple enzymatic conversions. The acetone formation pathway is depicted using dashed lines since acetone is not a common product of C. pasteurianum fermentations. The incomplete citrate cycle and other intermediary metabolic pathways are not depicted. Electron bifurcation by the Bcd-EtfAB enzyme complex is shown using 2NADH as reductant. Electron transfer via the EtfAB complex is not shown. Refer to main text for further discussion on central metabolic pathway enzymes and reactions. Abbreviations: EMPP, Embden-Meyerhof-Parnas pathway; N-O PPP, non-oxidative pentose phosphate pathway; MEDP, modified Entner-Doudoroff pathway; CFP, central fermentative pathways; PTS, phosphotransferase system; PMF, proton motive force; GFPC, glycerol facilitator protein channel; Glc, glucose; Suc, sucrose; Fru, fructose; DHA, dihydroxyacetone; 3-HPA, 3-hydroxypropionaldehyde; 1,3-PDO, 1,3-propanediol; GA, glyceraldehyde; FD OX , oxidized ferredoxin; FD RED , reduced ferredoxin.

    Journal: Scientific Reports

    Article Title: Genome-directed analysis of prophage excision, host defence systems, and central fermentative metabolism in Clostridium pasteurianum

    doi: 10.1038/srep26228

    Figure Lengend Snippet: Overview of the central metabolic pathways of C. pasteurianum based on genomic analysis. Prevalent metabolic pathways leading to production of acids (green), alcohols (blue), and gases (red) are shown derived from commonly employed growth substrates. Many arrows represent multiple enzymatic conversions. The acetone formation pathway is depicted using dashed lines since acetone is not a common product of C. pasteurianum fermentations. The incomplete citrate cycle and other intermediary metabolic pathways are not depicted. Electron bifurcation by the Bcd-EtfAB enzyme complex is shown using 2NADH as reductant. Electron transfer via the EtfAB complex is not shown. Refer to main text for further discussion on central metabolic pathway enzymes and reactions. Abbreviations: EMPP, Embden-Meyerhof-Parnas pathway; N-O PPP, non-oxidative pentose phosphate pathway; MEDP, modified Entner-Doudoroff pathway; CFP, central fermentative pathways; PTS, phosphotransferase system; PMF, proton motive force; GFPC, glycerol facilitator protein channel; Glc, glucose; Suc, sucrose; Fru, fructose; DHA, dihydroxyacetone; 3-HPA, 3-hydroxypropionaldehyde; 1,3-PDO, 1,3-propanediol; GA, glyceraldehyde; FD OX , oxidized ferredoxin; FD RED , reduced ferredoxin.

    Article Snippet: Spore titers have been reported to differ between seemingly identical strains of C. pasteurianum obtained from different culture collections (ATCC and DSM) , which could reflect variation in levels of excision of φ6013.

    Techniques: Derivative Assay, Modification, Peptide Mass Fingerprinting, Gas Chromatography

    Effect of substrate degree of reductance on the fermentation product profile of C. pasteurianum . Active metabolic pathways employed by the cell are shown during growth on a range of substrates possessing varied degrees of reductance. General catabolic equations are provided and show the number of moles of reducing equivalents generated (in bold) per two moles of pyruvate formed. Substrates and pathway intermediates are depicted as black and blue diamonds, respectively, while acid and alcohol products are shown as blue circles and squares, respectively. Trace products (

    Journal: Scientific Reports

    Article Title: Genome-directed analysis of prophage excision, host defence systems, and central fermentative metabolism in Clostridium pasteurianum

    doi: 10.1038/srep26228

    Figure Lengend Snippet: Effect of substrate degree of reductance on the fermentation product profile of C. pasteurianum . Active metabolic pathways employed by the cell are shown during growth on a range of substrates possessing varied degrees of reductance. General catabolic equations are provided and show the number of moles of reducing equivalents generated (in bold) per two moles of pyruvate formed. Substrates and pathway intermediates are depicted as black and blue diamonds, respectively, while acid and alcohol products are shown as blue circles and squares, respectively. Trace products (

    Article Snippet: Spore titers have been reported to differ between seemingly identical strains of C. pasteurianum obtained from different culture collections (ATCC and DSM) , which could reflect variation in levels of excision of φ6013.

    Techniques: Generated

    Identification and excision of phage φ6013 from the genome of C. pasteurianum . ( a ) Predicted excision mechanism of phage φ6013 from the genome of C. pasteurianum . Phage excision was induced by exposing exponential phase cultures of C. pasteurianum to 5 μg ml −1 mitomycin C, leading to recombination between attL and attR sites. Sequences corresponding to the core attL and attR φ6013 recombination sites are shown in uppercase. The resulting attP sequence of phage φ6013 is compared to the similar 12 nt core attP site of phage φ3626 from C. perfringens . Prophage excision leads to a circular 42,250 bp phage genome and a single attB scar site within the genome of C. pasteurianum . PCR primers for screening attL , attR , attP , and attB recombination sites are shown, as well as screening primers for long range PCR of the circular excised φ6013 genome. Genomes, genomic regions, and PCR primers are not depicted to scale. ( b ) PCR verification of phage φ6013 excision from the C. pasteurianum chromosome. Orientation and arrangement of PCR primers are depicted in Fig. 1a. Lane 1: marker; lane 2: 904 bp attL product (attLB.S + attL.AS); lane 3: 872 bp attR product (attRP.S + attRB.AS); lane 4: 3,154 bp attP product (attRP.S + attP.AS); lane 5: 1,076 bp attB product (attLB.S + attRB.AS); lane 6: long range PCR marker; lane 7: 22,756 bp 5′ φ6013 product (φ6013.S + attP.AS); lane 8: 22,678 bp 3′ φ6013 product (attRP.S + φ6013.AS). ( c ) Transmission electron microscopy image of phage φ6013 visualized at 245,000× magnification. ( d ) Genomic arrangement of phage φ6013 (42,250 bp). All 52 predicted genes, including some functional assignments, are depicted and are numbered consecutively. Genes in black and grey depict different directions of transcription. The predicted phage attachment site ( attP ) described in the main text is shown. All genes and intergenic regions are depicted to scale.

    Journal: Scientific Reports

    Article Title: Genome-directed analysis of prophage excision, host defence systems, and central fermentative metabolism in Clostridium pasteurianum

    doi: 10.1038/srep26228

    Figure Lengend Snippet: Identification and excision of phage φ6013 from the genome of C. pasteurianum . ( a ) Predicted excision mechanism of phage φ6013 from the genome of C. pasteurianum . Phage excision was induced by exposing exponential phase cultures of C. pasteurianum to 5 μg ml −1 mitomycin C, leading to recombination between attL and attR sites. Sequences corresponding to the core attL and attR φ6013 recombination sites are shown in uppercase. The resulting attP sequence of phage φ6013 is compared to the similar 12 nt core attP site of phage φ3626 from C. perfringens . Prophage excision leads to a circular 42,250 bp phage genome and a single attB scar site within the genome of C. pasteurianum . PCR primers for screening attL , attR , attP , and attB recombination sites are shown, as well as screening primers for long range PCR of the circular excised φ6013 genome. Genomes, genomic regions, and PCR primers are not depicted to scale. ( b ) PCR verification of phage φ6013 excision from the C. pasteurianum chromosome. Orientation and arrangement of PCR primers are depicted in Fig. 1a. Lane 1: marker; lane 2: 904 bp attL product (attLB.S + attL.AS); lane 3: 872 bp attR product (attRP.S + attRB.AS); lane 4: 3,154 bp attP product (attRP.S + attP.AS); lane 5: 1,076 bp attB product (attLB.S + attRB.AS); lane 6: long range PCR marker; lane 7: 22,756 bp 5′ φ6013 product (φ6013.S + attP.AS); lane 8: 22,678 bp 3′ φ6013 product (attRP.S + φ6013.AS). ( c ) Transmission electron microscopy image of phage φ6013 visualized at 245,000× magnification. ( d ) Genomic arrangement of phage φ6013 (42,250 bp). All 52 predicted genes, including some functional assignments, are depicted and are numbered consecutively. Genes in black and grey depict different directions of transcription. The predicted phage attachment site ( attP ) described in the main text is shown. All genes and intergenic regions are depicted to scale.

    Article Snippet: Spore titers have been reported to differ between seemingly identical strains of C. pasteurianum obtained from different culture collections (ATCC and DSM) , which could reflect variation in levels of excision of φ6013.

    Techniques: Sequencing, Polymerase Chain Reaction, Marker, Transmission Assay, Electron Microscopy, Functional Assay

    Amino acid sequence alignment of C. pasteurianum HydA (CpA) and C. acetobutylicum HydA (CaA) and HydB (CaB). The ClustalW algorithm was used to generate the alignment, and shading identifies identical (black) and similar (gray) residues. The N-terminal

    Journal:

    Article Title: Functional Studies of [FeFe] Hydrogenase Maturation in an Escherichia coli Biosynthetic System

    doi: 10.1128/JB.188.6.2163-2172.2006

    Figure Lengend Snippet: Amino acid sequence alignment of C. pasteurianum HydA (CpA) and C. acetobutylicum HydA (CaA) and HydB (CaB). The ClustalW algorithm was used to generate the alignment, and shading identifies identical (black) and similar (gray) residues. The N-terminal

    Article Snippet: Unlike C. acetobutylicum HydA, the C. acetobutylicum HydB amino acid sequence, shown in Fig. , has low sequence similarity to C. pasteurianum HydA, and the two are only 18.6% identical overall.

    Techniques: Sequencing, Cellular Antioxidant Activity Assay